I hate WebKit. I hate Blink, too, which is forked from it. The main issue I have with them is no matter which font our designer chooses, it always looks terrible on WebKit-based browsers. We're currently rebuilding our own website and we're using Lato which is available on Google Fonts. It looks great in Firefox, IE, and Opera, but the fonts are jagged and look bad on Chrome, Safari, and Opera Next (ever since it adopted Blink as its rendering engine). I've had this issue with personal projects for at least a year. From my research it has to do with anti-aliasing, but that's not something the web developer can control.
I have also noticed a weird issue with reactive websites with WebKit-based browsers that don't return elements back to their original position after resizing the window. It's very isolated and very peculiar, but I cannot reproduce the issue with non-WebKit-based browsers.
I prefer Gecko 10 times out of 10. Gecko is love. Gecko is life.
I am sure Gecko has its fair share of issues, but I have yet to run into anything major or noteworthy and Firefox is the browser I use by default since version 2.